Structural and sequence diversity of eukaryotic transposable elements

Abstract

The majority of eukaryotic genomes contain a large fraction of repetitive sequences that primarily originate from transpositional bursts of transposable elements (TEs). Repbase serves as a database for eukaryotic repetitive sequences and has now become the largest collection of eukaryotic TEs. During the development of Repbase, many new superfamilies/lineages of TEs, which include Helitron, Polinton, Ginger and SINEU, were reported. The unique composition of protein domains and DNA motifs in TEs sometimes indicates novel mechanisms of transposition, replication, anti-suppression or proliferation. In this review, our current understanding regarding the diversity of eukaryotic TEs in sequence, protein domain composition and structural hallmarks is introduced and summarized, based on the classification system implemented in Repbase. Autonomous eukaryotic TEs can be divided into two groups: Class I TEs, also called retrotransposons, and Class II TEs, or DNA transposons. Long terminal repeat (LTR) retrotransposons, including endogenous retroviruses, non-LTR retrotransposons, tyrosine recombinase retrotransposons and Penelope-like elements, are well accepted groups of autonomous retrotransposons. They share reverse transcriptase for replication but are distinct in the catalytic components responsible for integration into the host genome. Similarly, at least three transposition machineries have been reported in eukaryotic DNA transposons: DDD/E transposase, tyrosine recombinase and HUH endonuclease combined with helicase. Among these, TEs with DDD/E transposase are dominant and are classified into 21 superfamilies in Repbase. Non-autonomous TEs are either simple derivatives generated by internal deletion, or are composed of several units that originated independently.

AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi

“…In vertebrates, the genomes of some teleost fishes keep remnants of AcademHP copies. superfamily of DNA transposons, the lengths of TSDs are not so divergent [4,18]. Almost all of superfamilies show strict restriction of TSD lengths, which allows only 1-bp difference.…”

“…DNA transposons do not have a process of reverse transcription in their transposition cycle. At least 5 independent DNA-cleaving/recombining enzymes (DDE transposase or DDD/E transposase, tyrosine recombinase, serine recombinase, HUH nuclease, and Cas1 endonuclease) have been incorporated into TEs and related mobile genetic elements [4,5]. DDE transposase or integrase is the most ubiquitous enzyme that functions as transposase of DNA transposons, as well as of long terminal repeat (LTR) retrotransposons and of retroviruses [6].…”

Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

“…In ferns, the PBS is located 8 nt from the 5S rDNA sequence whereas in Brassica species it is up to 173 bp away. Therefore, we used following linked-sequences query in FASTA format to search both fern and seed plant genomes for Cassandra sequences: >Cassandra RGTTAAGYRHGY [15][16][17][18][19][20][21][22][23][24][25]RRRATRGGTRACY TGGTATCAGAGC.…”

The role of transposable elements in the ecological morphogenesis under the influence of stress

“…Class II includes DNA-TE, which are moved by "cut-and-paste" or "rolling circle". Their transposition is possible due to 3 different mechanisms: DDD/E transposase, tyrosine recombinase and endonuclease HUH in combination with helicase (Kojima, 2018). The most common TE classification is presented in Repbase (http://www.girinst.org/repbase/).…”